I manual shift mine all the time at the track and I run nitrous through it like it's the primary source of power - cause it is.
What you have to watch for is holding it in a gear too long. This causes heat.... so don't drive around in second to get the rumble of the exhaust unless you have one heck of a good tranny cooler.
If the thing has been properly built manual shifting won't hurt it. The hard shifting is actually good on the tranny to a point. Soft shifts cause friction and heat build up.
The thing you have to watch out for is O/D.... that thing is weak... I just had my tranny gone through again, but only because of O/D. If you shift at WOT into O/D you will slip the band and get it hot... over time the band wears down and then you'll be where I was and won't be able to climb a hill on the highway in O/D.
The question is, why so you feel it's shifting early when your not at WOT? If your not hot rodding it around, then it should be doing it's job just fine.
There are only 2 reasons I manual shift mine. One is I still haven't got it quite where my power points are. If I hold it another 300rpms in each gear I can get another couple tenths at the track each run.
The other is, If you've ever run the juice you might know this one, if you do a juice launch and your tires give enough to hit 4,500 rpms.... even though that's not the normal shift point at WOT the juice can confuse the tranny and the little bugger will shift into second on you. If you aren't rolling quite fast enough... second gear could be too high and you are putting a serious load on the car. Not good and can produce a lean condition in the car in a hurry.
I can't remember which video it is... but when the guys go...."oh, Paul" - it's not cause of the smoke, it's cause the tires hooked in 3rd and my car leaned out.
http://100mphclub.com/movies/psu_gcomfx2.mpg
http://100mphclub.com/movies/psu_gcomfx2.mpg